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Started:
October 27, 2022 17:05
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Completed:
17:05:19.000
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Failed:
No.
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Status:
completed
Events (most recent first):
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17:05:19.000
(ends)
Complete
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17:05:19.000
(ends)
TOTAL TIME: 13.537333607s
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17:05:19.000
(starts)
TraitBank::Denormalizer.update_resource_vernaculars
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17:05:19.000
(starts)
Running
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17:05:18.000
(starts)
Resource#fix_native_nodes
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17:05:18.000
(starts)
Running
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17:05:18.000
(warns)
Trait Publishing failed: At https://eol.org/data/microbe_ecomorp2/publish_traits.tsv @ position 126471 - there's a field starting with a quote and whereas it ends that quote there seems to be characters in that field after that ending quote. That isn't supported. This is what I read: 'Jaške, K., Barcytė, D., Pánek, T., Ševčíková, T., Eliášová, A., Eliáš, M., 2022. The net-like heterotrophic amoeba Leukarachnion salinum sp. nov. (Ochrophyta, Stramenopiles) has a cryptic plastid. bioRxiv.",https://doi.org/10.1101/2022.04.05.487141,,,,,
R1187-PK279498833,59245713,Rhodelphis,827e252a2b17409cf61cf1ec8ad65563_1664478464,http://eol.org/schema/terms/EcomorphologicalGuild,,,,,,http://www.wikidata.org/entity/Q113627402,http://www.wikidata.org/entity/Q113627402,,,,,,"BB' FROM /usr/local/bundle/bundler/gems/neo4j-ruby-driver-fe5438fb945d/ffi/neo4j/driver/internal/handlers/response_handler.rb:38:in `check_summary_failure' << /app/lib/trait_bank/slurp.rb:559:in `merge_triple' << /app/lib/trait_bank/slurp.rb:444:in `block in load_csv_where' << /app/lib/trait_bank/slurp.rb:444:in `each' << /app/lib/trait_bank/slurp.rb:444:in `load_csv_where' << /app/lib/trait_bank/slurp.rb:331:in `block (2 levels) in load_csv'
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17:05:18.000
(warns)
Exception (Neo4j::Driver::Exceptions::DatabaseException) FROM: #merge_triple QUERY: {USING PERIODIC COMMIT LOAD CSV WITH HEADERS FROM 'https://eol.org/data/microbe_ecomorp2/publish_traits.tsv' AS row WITH row WHERE 1=1
MATCH (page:Page { page_id: toInteger(row.page_id) })
MATCH (trait:Trait { eol_pk: row.eol_pk })}
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17:05:18.000
(warns)
Exception (Neo4j::Driver::Exceptions::DatabaseException) QUERY: {USING PERIODIC COMMIT LOAD CSV WITH HEADERS FROM 'https://eol.org/data/microbe_ecomorp2/publish_traits.tsv' AS row WITH row WHERE 1=1
MATCH (page:Page { page_id: toInteger(row.page_id) })
MATCH (trait:Trait { eol_pk: row.eol_pk })
MERGE (page)-[:trait]->(trait)} MESSAGE: At https://eol.org/data/microbe_ecomorp2/publish_traits.tsv @ position 126471 - there's a field starting with a quote and whereas it ends that quote there seems to be characters in that field after that ending quote. That isn't supported. This is what I read: 'Jaške, K., Barcytė, D., Pánek, T., Ševčíková, T., Eliášová, A., Eliáš, M., 2022. The net-like heterotrophic amoeba Leukarachnion salinum sp. nov. (Ochrophyta, Stramenopiles) has a cryptic plastid. bioRxiv.",https://doi.org/10.1101/2022.04.05.487141,,,,,
R1187-PK279498833,59245713,Rhodelphis,827e252a2b17409cf61cf1ec8ad65563_1664478464,http://eol.org/schema/terms/EcomorphologicalGuild,,,,,,http://www.wikidata.org/entity/Q113627402,http://www.wikidata.org/entity/Q113627402,,,,,,"BB'
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17:05:18.000
(warns)
Exception (Neo4j::Driver::Exceptions::DatabaseException) QUERY: {USING PERIODIC COMMIT LOAD CSV WITH HEADERS FROM 'https://eol.org/data/microbe_ecomorp2/publish_traits.tsv' AS row WITH row WHERE 1=1 MERGE (trait:Trait { eol_pk: row.eol_pk })
ON CREATE SET trait.resource_pk = row.resource_pk
ON MATCH SET trait.resource_pk = row.resource_pk
ON CREATE SET trait.source = row.source
ON MATCH SET trait.source = row.source
ON CREATE SET trait.literal = row.literal
ON MATCH SET trait.literal = row.literal
ON CREATE SET trait.measurement = row.measurement
ON MATCH SET trait.measurement = row.measurement
ON CREATE SET trait.scientific_name = row.scientific_name
ON MATCH SET trait.scientific_name = row.scientific_name
ON CREATE SET trait.normal_measurement = row.normal_measurement
ON MATCH SET trait.normal_measurement = row.normal_measurement
ON CREATE SET trait.sample_size = row.sample_size
ON MATCH SET trait.sample_size = row.sample_size
ON CREATE SET trait.citation = row.citation
ON MATCH SET trait.citation = row.citation
ON CREATE SET trait.remarks = row.remarks
ON MATCH SET trait.remarks = row.remarks
ON CREATE SET trait.method = row.method
ON MATCH SET trait.method = row.method} MESSAGE: At https://eol.org/data/microbe_ecomorp2/publish_traits.tsv @ position 126471 - there's a field starting with a quote and whereas it ends that quote there seems to be characters in that field after that ending quote. That isn't supported. This is what I read: 'Jaške, K., Barcytė, D., Pánek, T., Ševčíková, T., Eliášová, A., Eliáš, M., 2022. The net-like heterotrophic amoeba Leukarachnion salinum sp. nov. (Ochrophyta, Stramenopiles) has a cryptic plastid. bioRxiv.",https://doi.org/10.1101/2022.04.05.487141,,,,,
R1187-PK279498833,59245713,Rhodelphis,827e252a2b17409cf61cf1ec8ad65563_1664478464,http://eol.org/schema/terms/EcomorphologicalGuild,,,,,,http://www.wikidata.org/entity/Q113627402,http://www.wikidata.org/entity/Q113627402,,,,,,"BB'
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17:05:18.000
(warns)
FAILED on build_nodes query (Trait), will re-try once...
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17:05:18.000
(warns)
At https://eol.org/data/microbe_ecomorp2/publish_traits.tsv @ position 126471 - there's a field starting with a quote and whereas it ends that quote there seems to be characters in that field after that ending quote. That isn't supported. This is what I read: 'Jaške, K., Barcytė, D., Pánek, T., Ševčíková, T., Eliášová, A., Eliáš, M., 2022. The net-like heterotrophic amoeba Leukarachnion salinum sp. nov. (Ochrophyta, Stramenopiles) has a cryptic plastid. bioRxiv.",https://doi.org/10.1101/2022.04.05.487141,,,,,
R1187-PK279498833,59245713,Rhodelphis,827e252a2b17409cf61cf1ec8ad65563_1664478464,http://eol.org/schema/terms/EcomorphologicalGuild,,,,,,http://www.wikidata.org/entity/Q113627402,http://www.wikidata.org/entity/Q113627402,,,,,,"BB'
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17:05:18.000
(warns)
Exception (Neo4j::Driver::Exceptions::DatabaseException) QUERY: {USING PERIODIC COMMIT LOAD CSV WITH HEADERS FROM 'https://eol.org/data/microbe_ecomorp2/publish_traits.tsv' AS row WITH row WHERE 1=1 MERGE (trait:Trait { eol_pk: row.eol_pk })
ON CREATE SET trait.resource_pk = row.resource_pk
ON MATCH SET trait.resource_pk = row.resource_pk
ON CREATE SET trait.source = row.source
ON MATCH SET trait.source = row.source
ON CREATE SET trait.literal = row.literal
ON MATCH SET trait.literal = row.literal
ON CREATE SET trait.measurement = row.measurement
ON MATCH SET trait.measurement = row.measurement
ON CREATE SET trait.scientific_name = row.scientific_name
ON MATCH SET trait.scientific_name = row.scientific_name
ON CREATE SET trait.normal_measurement = row.normal_measurement
ON MATCH SET trait.normal_measurement = row.normal_measurement
ON CREATE SET trait.sample_size = row.sample_size
ON MATCH SET trait.sample_size = row.sample_size
ON CREATE SET trait.citation = row.citation
ON MATCH SET trait.citation = row.citation
ON CREATE SET trait.remarks = row.remarks
ON MATCH SET trait.remarks = row.remarks
ON CREATE SET trait.method = row.method
ON MATCH SET trait.method = row.method} MESSAGE: At https://eol.org/data/microbe_ecomorp2/publish_traits.tsv @ position 126471 - there's a field starting with a quote and whereas it ends that quote there seems to be characters in that field after that ending quote. That isn't supported. This is what I read: 'Jaške, K., Barcytė, D., Pánek, T., Ševčíková, T., Eliášová, A., Eliáš, M., 2022. The net-like heterotrophic amoeba Leukarachnion salinum sp. nov. (Ochrophyta, Stramenopiles) has a cryptic plastid. bioRxiv.",https://doi.org/10.1101/2022.04.05.487141,,,,,
R1187-PK279498833,59245713,Rhodelphis,827e252a2b17409cf61cf1ec8ad65563_1664478464,http://eol.org/schema/terms/EcomorphologicalGuild,,,,,,http://www.wikidata.org/entity/Q113627402,http://www.wikidata.org/entity/Q113627402,,,,,,"BB'
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17:05:18.000
(warns)
Exception (Neo4j::Driver::Exceptions::DatabaseException) QUERY: {USING PERIODIC COMMIT LOAD CSV WITH HEADERS FROM 'https://eol.org/data/microbe_ecomorp2/publish_traits.tsv' AS row WITH row WHERE 1=1 MERGE (page:Page { page_id: toInteger(row.page_id) })} MESSAGE: At https://eol.org/data/microbe_ecomorp2/publish_traits.tsv @ position 126471 - there's a field starting with a quote and whereas it ends that quote there seems to be characters in that field after that ending quote. That isn't supported. This is what I read: 'Jaške, K., Barcytė, D., Pánek, T., Ševčíková, T., Eliášová, A., Eliáš, M., 2022. The net-like heterotrophic amoeba Leukarachnion salinum sp. nov. (Ochrophyta, Stramenopiles) has a cryptic plastid. bioRxiv.",https://doi.org/10.1101/2022.04.05.487141,,,,,
R1187-PK279498833,59245713,Rhodelphis,827e252a2b17409cf61cf1ec8ad65563_1664478464,http://eol.org/schema/terms/EcomorphologicalGuild,,,,,,http://www.wikidata.org/entity/Q113627402,http://www.wikidata.org/entity/Q113627402,,,,,,"BB'
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17:05:18.000
(warns)
FAILED on build_nodes query (Page), will re-try once...
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17:05:18.000
(warns)
At https://eol.org/data/microbe_ecomorp2/publish_traits.tsv @ position 126471 - there's a field starting with a quote and whereas it ends that quote there seems to be characters in that field after that ending quote. That isn't supported. This is what I read: 'Jaške, K., Barcytė, D., Pánek, T., Ševčíková, T., Eliášová, A., Eliáš, M., 2022. The net-like heterotrophic amoeba Leukarachnion salinum sp. nov. (Ochrophyta, Stramenopiles) has a cryptic plastid. bioRxiv.",https://doi.org/10.1101/2022.04.05.487141,,,,,
R1187-PK279498833,59245713,Rhodelphis,827e252a2b17409cf61cf1ec8ad65563_1664478464,http://eol.org/schema/terms/EcomorphologicalGuild,,,,,,http://www.wikidata.org/entity/Q113627402,http://www.wikidata.org/entity/Q113627402,,,,,,"BB'
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17:05:18.000
(warns)
Exception (Neo4j::Driver::Exceptions::DatabaseException) QUERY: {USING PERIODIC COMMIT LOAD CSV WITH HEADERS FROM 'https://eol.org/data/microbe_ecomorp2/publish_traits.tsv' AS row WITH row WHERE 1=1 MERGE (page:Page { page_id: toInteger(row.page_id) })} MESSAGE: At https://eol.org/data/microbe_ecomorp2/publish_traits.tsv @ position 126471 - there's a field starting with a quote and whereas it ends that quote there seems to be characters in that field after that ending quote. That isn't supported. This is what I read: 'Jaške, K., Barcytė, D., Pánek, T., Ševčíková, T., Eliášová, A., Eliáš, M., 2022. The net-like heterotrophic amoeba Leukarachnion salinum sp. nov. (Ochrophyta, Stramenopiles) has a cryptic plastid. bioRxiv.",https://doi.org/10.1101/2022.04.05.487141,,,,,
R1187-PK279498833,59245713,Rhodelphis,827e252a2b17409cf61cf1ec8ad65563_1664478464,http://eol.org/schema/terms/EcomorphologicalGuild,,,,,,http://www.wikidata.org/entity/Q113627402,http://www.wikidata.org/entity/Q113627402,,,,,,"BB'
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17:05:16.000
(infos)
Importing 128000 rows from publish_traits.tsv
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17:05:16.000
(infos)
adding new traits
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17:05:16.000
(infos)
removing all traits
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17:05:16.000
(infos)
Connecting to https://content.eol.org/ ...
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17:05:15.000
(infos)
Connecting to https://content.eol.org/ ...
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17:05:15.000
(infos)
polling for trait diff metadata: /resources/1187/publish_diffs.json
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17:05:15.000
(starts)
#publish_traits = TraitBank::Slurp.load_resource_from_repo
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17:05:15.000
(starts)
Running
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17:05:15.000
(warns)
There were NO new pages, skipping...
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17:05:14.000
(starts)
create_new_pages
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17:05:14.000
(starts)
PageCreator
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17:05:14.000
(starts)
Running
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17:05:14.000
(starts)
restoring vernacular preferences...
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17:05:14.000
(starts)
Running
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17:05:14.000
(warns)
MISSING https://content.eol.org/data/microbe_ecomorp2/publish_content_sections.tsv [404] (8 bytes); skipping
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17:05:13.000
(infos)
Connecting to https://content.eol.org/ ...
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17:05:13.000
(starts)
#grab_file content_sections.tsv
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17:05:13.000
(starts)
Running
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17:05:13.000
(starts)
#import_and_prop_ids ContentSection
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17:05:13.000
(starts)
Running
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17:05:13.000
(warns)
MISSING https://content.eol.org/data/microbe_ecomorp2/publish_references.tsv [404] (8 bytes); skipping
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17:05:13.000
(infos)
Connecting to https://content.eol.org/ ...
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17:05:13.000
(starts)
#grab_file references.tsv
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17:05:13.000
(starts)
Running
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17:05:13.000
(starts)
#import_and_prop_ids Reference
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17:05:13.000
(starts)
Running
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17:05:13.000
(warns)
MISSING https://content.eol.org/data/microbe_ecomorp2/publish_image_info.tsv [404] (8 bytes); skipping
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17:05:13.000
(infos)
Connecting to https://content.eol.org/ ...
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17:05:13.000
(starts)
#grab_file image_info.tsv
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17:05:13.000
(starts)
Running
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17:05:13.000
(starts)
#import_and_prop_ids ImageInfo
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17:05:13.000
(starts)
Running
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17:05:13.000
(warns)
MISSING https://content.eol.org/data/microbe_ecomorp2/publish_attributions.tsv [404] (8 bytes); skipping
